Nonlinear vs. linear biasing in Trp-cage folding simulations

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F15%3A43899754" target="_blank" >RIV/60461373:22330/15:43899754 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14610/15:00080979

Výsledek na webu

<a href="http://scitation.aip.org/content/aip/journal/jcp/142/11/10.1063/1.4914828" target="_blank" >http://scitation.aip.org/content/aip/journal/jcp/142/11/10.1063/1.4914828</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1063/1.4914828" target="_blank" >10.1063/1.4914828</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Nonlinear vs. linear biasing in Trp-cage folding simulations

Popis výsledku v původním jazyce

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionalityreduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In ter

Název v anglickém jazyce

Nonlinear vs. linear biasing in Trp-cage folding simulations

Popis výsledku anglicky

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionalityreduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In ter

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CE - Biochemie

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2015

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Chemical Physics

ISSN

0021-9606

e-ISSN

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Svazek periodika

142

Číslo periodika v rámci svazku

11

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

8

Strana od-do

115101

Kód UT WoS článku

000351530100042

EID výsledku v databázi Scopus

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